Monthly Archives: January 2014

MINT, Intact, MINTACT, and other protein interactions databases

Protein-protein interactions are stored in public databases. Many of them exists, but only a few capture enough experimental information to allow for evaluating the data quality, or even what kind of interaction has been described.

In a recent review (Towards a detailed atlas of protein–protein interactions) I commented about the level of curation and the databases which allow for instance to distinguish binary interactions. MINT, Intact and DIP are three of those.

MINT has always been my favourite one: I worked on it for many years. I believe it has one of the most user friendly interfaces (check this OpenHelix post about how it is “so fun to use”). It was also appreciated by wet laboratories for the data it contains. Indeed one of the particularity of MINT is that it is run by a wet-lab group (the group of Gianni Cesareni at the University of Rome) and the data is often curated according to the needs of the laboratory. In the past it permits to extends the coverage of domain mediated interactions or protein interactions in viruses.

Recently, with the name of “MINTACT” project, MINT and Intact announced that the interactions curated by the MINT staff will be directly inserted into Intact. While it first sounded like the death of MINT, it isn’t yet. While the future of the web interface in uncertain (the MINT group has recently developed a new interface called mentha to aggregate interactions from different databases), the curation staff is still working. If you prefer submit your interaction data to MINT, you can still do it. MINT curators will process your data as they used to do. The big advantage on the user side is that it will be automatically incorporated with Intact. Downloading data from Intact (or using the really useful psicquic REST server from Intact) will provides access to both MINT and Intact. The update of the data  will also be ensured by the Intact team (MINT data, because of the low human resources of the group, was not as updated as Intact’s one).

Other databases were already sending their data directly in Intact. As a consequence, all IMEx interactions, except the ones from DIP, are stored and available with all the detailed information in Intact.

I recommend reading the MINTACT paper for more information.


Blogging about Genomics and Network Biology

I’m starting today this blog about what I’m currently doing: Genomics, Network Biology (particularly Protein Interaction Networks), and how to go from one to the other. I’ll report here on my works, the tools I’m using or about what other people are doing and sounds interesting to me.